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- PDB-5tje: Murine class I major histocompatibility complex H-2Db in complex ... -

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Basic information

Entry
Database: PDB / ID: 5tje
TitleMurine class I major histocompatibility complex H-2Db in complex with LCMV-derived gp33 and T cell receptor P14
Components
  • ALPHA CHAIN OF MURINE T CELL RECEPTOR p14
  • BETA CHAIN OF MURINE T CELL RECEPTOR p14
  • Beta-2-microglobulin
  • H-2 class I histocompatibility antigen, D-B alpha chain
  • Peptide gp33-41 from LCMV
KeywordsIMMUNE SYSTEM / T Cell Receptor / MHC class I / LCMV / protein-protein interaction
Function / homology
Function and homology information


Endosomal/Vacuolar pathway / DAP12 interactions / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / ER-Phagosome pathway / DAP12 signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / host cell Golgi membrane / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / beta-2-microglobulin binding / cellular defense response ...Endosomal/Vacuolar pathway / DAP12 interactions / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / ER-Phagosome pathway / DAP12 signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / host cell Golgi membrane / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / beta-2-microglobulin binding / cellular defense response / Neutrophil degranulation / antigen processing and presentation of endogenous peptide antigen via MHC class Ib / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent / lumenal side of endoplasmic reticulum membrane / peptide binding / cellular response to iron(III) ion / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / negative regulation of forebrain neuron differentiation / regulation of erythrocyte differentiation / peptide antigen assembly with MHC class I protein complex / regulation of iron ion transport / response to molecule of bacterial origin / MHC class I peptide loading complex / HFE-transferrin receptor complex / T cell mediated cytotoxicity / positive regulation of T cell cytokine production / antigen processing and presentation of endogenous peptide antigen via MHC class I / MHC class I protein complex / negative regulation of neurogenesis / positive regulation of receptor-mediated endocytosis / peptide antigen assembly with MHC class II protein complex / multicellular organismal-level iron ion homeostasis / MHC class II protein complex / cellular response to nicotine / positive regulation of cellular senescence / positive regulation of T cell mediated cytotoxicity / phagocytic vesicle membrane / peptide antigen binding / antigen processing and presentation of exogenous peptide antigen via MHC class II / negative regulation of epithelial cell proliferation / positive regulation of immune response / positive regulation of T cell activation / sensory perception of smell / negative regulation of neuron projection development / MHC class II protein complex binding / late endosome membrane / iron ion transport / T cell differentiation in thymus / protein refolding / protein homotetramerization / intracellular iron ion homeostasis / amyloid fibril formation / receptor-mediated endocytosis of virus by host cell / learning or memory / host cell endoplasmic reticulum membrane / immune response / lysosomal membrane / external side of plasma membrane / signaling receptor binding / fusion of virus membrane with host endosome membrane / viral envelope / protein-containing complex binding / virion attachment to host cell / host cell plasma membrane / structural molecule activity / virion membrane / Golgi apparatus / protein homodimerization activity / extracellular space / membrane / metal ion binding / plasma membrane / cytosol
Similarity search - Function
Arenavirus glycoprotein, zinc binding domain / Arenavirus glycoprotein / Arenavirus glycoprotein / MHC class I, alpha chain, C-terminal / MHC_I C-terminus / MHC class I-like antigen recognition-like / Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 / MHC class I alpha chain, alpha1 alpha2 domains / Class I Histocompatibility antigen, domains alpha 1 and 2 / Beta-2-Microglobulin ...Arenavirus glycoprotein, zinc binding domain / Arenavirus glycoprotein / Arenavirus glycoprotein / MHC class I, alpha chain, C-terminal / MHC_I C-terminus / MHC class I-like antigen recognition-like / Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 / MHC class I alpha chain, alpha1 alpha2 domains / Class I Histocompatibility antigen, domains alpha 1 and 2 / Beta-2-Microglobulin / : / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like superfamily / MHC classes I/II-like antigen recognition protein / : / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Beta-2-microglobulin / H-2 class I histocompatibility antigen, D-B alpha chain / Pre-glycoprotein polyprotein GP complex
Similarity search - Component
Biological speciesMus musculus (house mouse)
Lymphocytic choriomeningitis virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsAchour, A. / Sandalova, T. / Allerbring, E. / Popov, A.
CitationJournal: to be published
Title: Thernary complexes of TCR P14 give insights into the mechanisms behind reestablishment of CTL responses against a viral escape mutant
Authors: Allerbring, E. / Duru, A.D. / Sun, R. / Han, X. / Uchtenhagen, H. / Madhurantakam, C. / Popov, A. / Markova, N. / Talyzina, A. / Nygren, P.A. / Sandalova, T. / Achour, A.
History
DepositionOct 4, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Nov 1, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: H-2 class I histocompatibility antigen, D-B alpha chain
B: Beta-2-microglobulin
C: H-2 class I histocompatibility antigen, D-B alpha chain
D: Beta-2-microglobulin
G: ALPHA CHAIN OF MURINE T CELL RECEPTOR p14
H: BETA CHAIN OF MURINE T CELL RECEPTOR p14
E: ALPHA CHAIN OF MURINE T CELL RECEPTOR p14
F: BETA CHAIN OF MURINE T CELL RECEPTOR p14
I: Peptide gp33-41 from LCMV
J: Peptide gp33-41 from LCMV


Theoretical massNumber of molelcules
Total (without water)189,11510
Polymers189,11510
Non-polymers00
Water48627
1
A: H-2 class I histocompatibility antigen, D-B alpha chain
B: Beta-2-microglobulin
G: ALPHA CHAIN OF MURINE T CELL RECEPTOR p14
H: BETA CHAIN OF MURINE T CELL RECEPTOR p14
I: Peptide gp33-41 from LCMV


Theoretical massNumber of molelcules
Total (without water)94,5585
Polymers94,5585
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: H-2 class I histocompatibility antigen, D-B alpha chain
D: Beta-2-microglobulin
E: ALPHA CHAIN OF MURINE T CELL RECEPTOR p14
F: BETA CHAIN OF MURINE T CELL RECEPTOR p14
J: Peptide gp33-41 from LCMV


Theoretical massNumber of molelcules
Total (without water)94,5585
Polymers94,5585
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)61.174, 66.943, 525.391
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
12B
22D
13G
23E
14H
24F
15I
25J

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1111A1 - 276
2111C1 - 276
1121B1 - 99
2121D1 - 99
1131G1 - 180
2131E1 - 180
1141H1 - 120
2141F1 - 120
1151I1 - 9
2151J1 - 9

NCS ensembles :
ID
1
2
3
4
5

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(0.06214, -0.975727, -0.20999), (-0.976111, -0.103301, 0.191144), (-0.208196, 0.193096, -0.958837)-44.84616, -20.91044, -129.17117

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Components

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Protein , 4 types, 8 molecules ACBDGEHF

#1: Protein H-2 class I histocompatibility antigen, D-B alpha chain / H-2D(B)


Mass: 32087.703 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: H2-D1
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P01899
#2: Protein Beta-2-microglobulin


Mass: 11704.359 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: B2m / Production host: Escherichia coli (E. coli) / References: UniProt: P01887
#3: Protein ALPHA CHAIN OF MURINE T CELL RECEPTOR p14


Mass: 23072.697 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli)
#4: Protein BETA CHAIN OF MURINE T CELL RECEPTOR p14


Mass: 26647.633 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli)

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Protein/peptide / Non-polymers , 2 types, 29 molecules IJ

#5: Protein/peptide Peptide gp33-41 from LCMV


Mass: 1045.232 Da / Num. of mol.: 2 / Mutation: C41M / Source method: obtained synthetically / Source: (synth.) Lymphocytic choriomeningitis virus / References: UniProt: Q9QDK7*PLUS
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 27 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.84 Å3/Da / Density % sol: 56.75 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 0.1M TRIS HCL PEG 6000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 30, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 3.2→39 Å / Num. obs: 35190 / % possible obs: 96.1 % / Redundancy: 3.2 % / Rmerge(I) obs: 0.17 / Net I/σ(I): 5.8
Reflection shellResolution: 3.2→3.37 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.71 / Mean I/σ(I) obs: 1.7 / % possible all: 98.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0124refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1S7U

1s7u


Resolution: 3.2→38.88 Å / Cor.coef. Fo:Fc: 0.9 / Cor.coef. Fo:Fc free: 0.789 / SU B: 36.824 / SU ML: 0.611 / Cross valid method: THROUGHOUT / ESU R Free: 0.619 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.31375 1825 5.2 %RANDOM
Rwork0.22765 ---
obs0.23204 33273 94.74 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 78.648 Å2
Baniso -1Baniso -2Baniso -3
1-0.96 Å20 Å2-0 Å2
2---1.31 Å20 Å2
3---0.35 Å2
Refinement stepCycle: 1 / Resolution: 3.2→38.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11757 0 0 27 11784
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.01912093
X-RAY DIFFRACTIONr_bond_other_d0.0030.0210970
X-RAY DIFFRACTIONr_angle_refined_deg1.7291.93216417
X-RAY DIFFRACTIONr_angle_other_deg1.093325273
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.59751447
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.34523.689599
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.46151949
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.8691579
X-RAY DIFFRACTIONr_chiral_restr0.0910.21703
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02113733
X-RAY DIFFRACTIONr_gen_planes_other0.0030.022960
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it6.6317.6945827
X-RAY DIFFRACTIONr_mcbond_other6.6297.6945826
X-RAY DIFFRACTIONr_mcangle_it10.61311.5147261
X-RAY DIFFRACTIONr_mcangle_other10.61311.5147262
X-RAY DIFFRACTIONr_scbond_it6.2948.0876266
X-RAY DIFFRACTIONr_scbond_other6.2948.0876266
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other10.09311.9799156
X-RAY DIFFRACTIONr_long_range_B_refined15.18761.00613215
X-RAY DIFFRACTIONr_long_range_B_other15.18761.00613216
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 2 / Refine-ID: X-RAY DIFFRACTION / Type: tight thermal / Weight position: 0.5

Ens-IDAuth asym-IDNumberRms dev position (Å)
1C43139.41
2D15847.48
3E16768.71
4F17947.29
5J1455.5
LS refinement shellResolution: 3.2→3.283 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.379 150 -
Rwork0.352 2389 -
obs--97.65 %

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